Trustwave PCI Failed - 3 Issues

I have the following 3 failed notification on a new server that I am trying to resolve. I believe that I have tried all the methods I have been able to find through other threads. Amy help would be great.

The cross site scripting, if valid, is likely an issue in the hosted application (website) itself. The report should have steps to reproduce that issue. Often those can be false positives but you should have the web dev have a good look at it. The other ones we would need to know what service/port number is associated with them in order to help.